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Bio-EnsEMBL-112.0.0_58
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/ Bio::EnsEMBL::CDS

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::CDS - Object representing a CDS

SYNOPSIS

use Bio::EnsEMBL::CDS;

$feature = Bio::EnsEMBL::CDS->new(
  -start         => 100,
  -end           => 220,
  -strand        => -1,
  -slice         => $slice,
  -phase         => 1,
  -transcript    => $transcript
);

DESCRIPTION

This is a CDS feature within the Ensembl CDS. It represents the coding regions of a transcript.

METHODS

new

Arg [...]  : Named arguments passed to superclass
Example    : $feature = Bio::EnsEMBL::CDS->new
                      (-start   => 1,
                       -end     => 100,
                       -strand  => 1,
                       -slice   => $slice,
                       -dbID    => 10,
                       -transcript  => $transcript,
                       -phase   => 1);
Description: Constructs a new Bio::EnsEMBL::CDS.
Returntype : Bio::EnsEMBL::CDS
Exceptions : Thrown on invalid -SLICE, -STRAND arguments
Caller     : general, subclass constructors
Status     : Stable

transcript

Arg [1]    : (optional) Bio::EnsEMBL::Transcript
Example    : $transcript = $cds->transcript();
Description: Getter/Setter for the transcript associated with this
             CDS.
Returntype : Bio::EnsEMBL::Transcript
Exceptions : none
Caller     : general
Status     : Stable

translation

Description: Fetch the translation associated with
             this transcript, if it exists. Return undef
             if there is no translation, ie. a pseudogene
Returntype : Bio::EnsEMBL::Translation or undef
Caller     : general
Status     : Stable

seq_region_start

Arg [1]    : (optional) string $seq_region_start
Example    : $seq_region_start = $cds->seq_region_start();
Description: Getter/Setter for the seq_region_start for this CDS.
             Overwrite default method from Feature as CDS does not have
             a table
Returntype : String
Exceptions : none
Caller     : general
Status     : Stable

seq_region_end

Arg [1]    : (optional) string $seq_region_end
Example    : $seq_region_end = $cds->seq_region_end();
Description: Getter/Setter for the seq_region_end for this CDS.
             Overwrite default method from Feature as CDS does not have
             a table
Returntype : String
Exceptions : none
Caller     : general
Status     : Stable

get_Gene

Description: Get the gene associated with the ExonTranscript,
             if a transcript has been set
Returntype : Bio::EnsEMBL::Gene or undef
Exceptions : none
Caller     : general
Status     : Stable

translation_id

Arg [1]    : (optional) string $translation_id
Example    : $translation_id = $cds->translation_id();
Description: Getter/Setter for the stable_id for the translation
             associated with this CDS.
Returntype : String
Exceptions : none
Caller     : general
Status     : Stable

phase

Arg [1]    : (optional) string $phase
Example    : print $cds->phase();
Description: This method returns an integer that describes
             the phase of the coding feature
Returntype : integer
Exceptions : none
Caller     : general
Status     : Stable

summary_as_hash

Example    : my $hash = $cds->summary_as_hash();
Description: Generates a HashRef compatible with GFFSerializer. Adds
             Parent, source and phase to the basic feature hash
Returntype : Hash
Exceptions : none
Caller     : general
Status     : Stable